Hidden Secrets
by AgentMaryMargaretSkitz
Summary: [Still THE PHOTOGRAPH] While at Providence, Grant Ward receives an interesting item. Four months later, the team is getting back on their feet, with things actually looking up for them for once. That is, until a second traitor is discovered, Skye and Fitz are kidnapped, and secrets surrounding Skye's past begin to come out, revealing shocking truths.
1. Chapter 1

**I own nothing relating to Agents of SHIELD or Marvel in anyway, unless a Cap shield counts.**

**The original idea for this was going to be an alternate universe after Providence with Jemma being Hydra and Skye and Fitz running off to go trace down her past, yada yada yada. However, while I was still in the first chapter, I changed my mind about some stuff, and decided it would work out better.**

**The likelihood of this ever occurring is less than one percent, but it would be cool it did.**

* * *

Prologue: A Meeting in the Closet

He didn't expect to be pulled into a room while walking around in Providence. But the sudden change of scenery sent his instincts into motion, and he lashed out with his fist. His knuckles connected with air, and he stumbled a little. As he turned to strike elsewhere, a sharp hit to his ribs sent him doubling over.

"So how's Raina?"

Ward wasn't as surprised at the question as he was by the person who asked it. "What are you talking about?"

She closed the door behind them. They appeared to be in a storage closet of some sort. He couldn't hold back the memory of another closet, only he had been with Skye then.

"Don't lie to me," said Simmons, her voice low and dark. "I know you didn't go drop off Garrett at the Fridge. I bet you were even one of those lucky few who got to raid it. I also know that Raina's out. I've worked with her before, and I know that scent of perfume anywhere. It might have been faint when you arrived, but I was close enough to you to smell it. So cut the bull, Ward."

Ward looked at her. This was a side of Jemma Simmons he didn't know existed. "What do you know?"

She shrugged. "I know you are Hydra, and that you came into it under Agent Garrett. I know that you're not here because of your loyalty to the remains of what was once called SHIELD, but because Garrett wants something. Whether it's murdering everyone here or exposing this little haven to Hydra, I don't know. But I know that it has something to do with Coulson's team."

Damn she was good. She had caught things that he had not expected. But something in the sentence that she just said sounded off. "You said Coulson's team. Not my team."

"You're very observant Agent Ward."

"You're not SHIELD."

She shook her head, smiling. "You'd be surprised at the number of people who are only loyal to SHIELD. It's quite shocking to see how many of those 'loyal' agents have ulterior motives."

Ward felt his breath catch. Did he have an ally in his midst? "Are you Hydra?" he asked hesitantly. Right now, she could say almost anything and surprise him.

Simmons scoffed, offended. Her lip curled in disgust. "No, I'm invested in something much more advanced and much less sloppy than Hydra. I'm part of something that's built to last. Raina is too, even if her current objective lies within Hydra. Which is why I need you."

Her eyes shone with pride and admiration as she spoke. Ward wished he could be that passionate about Hydra's goals. But his first loyalty was Garrett. It had always been for the man who pulled him out of his hell.

"What do you want?" he asks flatly, swallowing a little.

Smiling sweetly, she reached into her pocket and produced a piece of paper. She handed it to him. Turning it over, Ward saw it was a photograph of someone he knew all too well. "This is-"

Her hand clapped over his mouth. "Hush now," she scolded. "All I need you to do is give this to Raina as soon as you return to the Hydra base."

He blinked. "But what does she want with this?" Unless Raina had some creepy obsession he was unaware of, he didn't know how the photo would come of use to her.

"There's someone who's been looking for her for a long time, Agent Ward," Simmons said casually. "They want to know what she can do. I'm just passing intel up to someone who is closer to the top than myself."

Ward gripped the photograph. "You know, I can expose you to the team."

Simmons laughed, but it was an icy laugh that almost made him shiver. "I can do the same thing, Grant," she said, her words precise and cutting. "And somehow, I think they would be more inclined to believe me if I show the footage from the Fridge."

She held up a flash drive he had never seen before. Ward felt nervous, but considered the possibility that she could be lying. But he couldn't tell anymore. The warm, bubbly biochemist was gone, replaced instead by this cold woman who knew things that could destroy him. She was right though; he couldn't just walk up and expose her. He didn't even what or who she really worked for.

Ward slipped the photo into his pocket and made for the door. Before he could grab the handle, Simmons darted in front and stopped him. "Simmons, please," he whispered pleadingly. He wanted to get out and get away from her. She actually scared him now.

"You say _nothing_ of this," she hissed. "You even give so much as hint of what I really am, and I swear whatever hell you've gone through with your parents or Garrett will be like heaven compared to what I could do to you. Are we clear?"

He nodded. Simmons smiled brightly as the mask of the cheery Brit slid back onto her features.

"Let's go rejoin the team before they begin to wonder about us." She opened the door, her face a picture of innocence. "Shall we?"

* * *

"Simmons wanted you to have this."

Raina nodded in thanks at the specialist who had just handed her the photograph. Ward then left the room to go find Garrett or someone else. She didn't care who. It didn't matter to her.

Looking at the photo made her stomach turn with fear. She remembered the last time she met Skye, when she had been torturing Coulson for information, the girl had punched her. But the memory of that incident wasn't what made her so scared. It was knowing what she could be to her and what he might do to her that really scared Raina. It was for this reason that she hoped for once in her life that Jemma Simmons was actually wrong, and that Skye wasn't who she thought she was.

* * *

**Hee hee hee. Hope you all like this prologue. Dark Jemma is something I really wanted to see, and I like her now even better that she and Ward aren't doing Hydra crap together like I had originally planned.**

**Raina is going to have a pretty big role in this. I've been fascinated with her character ever since The Magical Place, and that fascination, along with this idea, grew after Providence.**

**Please review and tell me what you think!**


	2. Chapter 2

**I'm guessing people are pretty excited for this, and I am too so far. Thanks for all the response!**

**I'm pretty glad I edited the direction of the story, although I did have to lose a really powerful scene involving Raina. I've gotta to tell you guys, I really can't wait to push Raina into this more because I love what I've done with her in this!**

**A lot of people are intrigued by Dark Jemma, as I've come to call her. Making her what she is in this instead of Hydra was one of the better decisions I've ever made. I hope you all like the plans I have in store for her. Unfortunately, you don't get to see what she's up to in this chapter, but the next will provide some more of her being sinister.**

**So, this is four months after the finale, and things are looking pretty good for everyone. And because I'm a sap and it's pretty awesome for the plot, my Scottish science babe is alright. You guys might try to call me out on some possible Skitz, but I'm probably not going to go down that road. Maybe, I don't know though. Possibly not. Augh, I don't know yet. Just read this chapter, review, tell me what you think.**

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Chapter 1: 4 Months Later

"I found your daughter."

Raina watched him closely as he studied the photograph. His hands were covered in blood, and she shivered a little inside. His hands were always covered in blood, even when they were clean. No matter how hard he scrubbed, she still knew there was always going to be blood on his hands.

A smile crept across his face. "Who gave you this?"

"Simmons." She kept her answer short, clear and precise. The sooner she was gone, the better she would feel.

He looked at her, and her stomach twisted in hate. "Jemma is rarely wrong."

"_Please let her be for once."_ Raina thought silently. If it was true, if Skye was who he thought she was, then Raina would do whatever it took to protect her, and if she failed, then there would be more blood on her hands, more personal blood. "No one is perfect."

"One day, we will all be perfect, Raina."

The girl flinched. She hated that name, but he had demanded that she take it when she went to investigate the Clairvoyant. Her real name was something he only called her when things were serious.

"You know she's more than just my daughter," he continued, smiling at the photograph hungrily. "Especially to you."

Raina bit her lip, holding back anger. She didn't want to believe it. It would be the worst thing ever if it was true. It would condemn Skye to tests and experiments, a life she herself had been forced into by fear. Skye deserved happiness and freedom and blissful ignorance of this horror, and she would do whatever it took to ensure she stayed away from all of this.

"Well forgive me for losing my faith," she snarled. "After all those other times we've been wrong before, I don't know if this one's the right one either."

With that she left the room. She hated this thing. Every time he thought he'd found her before, he'd been wrong and another innocent had died. Raina didn't want to believe that Skye was the one they'd searched so long for, but the little voice in the back of her head kept pointing out the possibilities.

"_Please,"_ she thought silently. _"Please don't let her be Tian Kong."_

* * *

_Four months later_

Skye couldn't help but chuckle as she hit the mat once more. It always made her laugh when she sparred with him. After four months of training with May, there weren't a lot of people out there who could knock her down. However, the fact that she could sometimes befriend the floor when she sparred with one particular person just made her giggle.

"Why do you always do that?" Her partner asked, holding out a hand. Skye grasped it, and Leo Fitz pulled her up.

"Because four months ago, you are the last person who I thought could take me down," laughed Skye. She walked over to the bench in the Playground's gym and tossed him his water bottle.

It had been four months since they had landed at the Playground base and began their work to re-build SHIELD. During the first month they'd been there, Leo had been in a coma thanks to his trip to the bottom of the ocean. Then halfway in the second month, he'd miraculously woken up without any negative side effects from his coma. He had full control of his body, his motor skills were intact, and his memory was unscathed. It was as if he'd only slept ten hours instead of waking up from an almost two month coma.

After he'd awoken and had been cleared by Simmons, Leo had asked Tripp to train him. He wanted to know how to protect and defend himself. To go on the offensive instead of running away. So Tripp had taken him under his wing, and helped him. Over the course of two months filled with rigorous training, Leo Fitz had become quite capable of defending himself. He had also developed a fine set of abs and stronger muscle definition that his blue-gray exercise shirt displayed quite nicely. Not that Skye had ever been staring at him lately. Which she hadn't.

In the month that he'd first started to work out, Leo and Simmons had kind of been dating since he had confessed having feelings for her before they escaped the med pod. Skye had been happy for Simmons when she had told her, but also a little sad and jealous. She wasn't sure why, but attributed it to Ward and his betrayal. However, the romance had only lasted a month with them deciding they were better off as best friends and lab partners. Skye was surprised that both of them took the break-up very well. She couldn't even tell who had broken up with whom. But Leo later confided after a joint-training session with her that he'd been the one who talked to her first about it, and she had agreed.

Joint-training sessions with Leo and Trip had become more common recently, and Skye liked them better than training alone with May. When she was alone with May, the older woman was quieter than usual, more reluctant. Almost, and Skye couldn't believe she could ever associate the word with someone like May, scared. There was a sad look in her eyes sometimes too, like she was remembering something, but more often there would be moments where she almost hesitated when she sparred with Skye.

Her status as an 084 was mostly likely the blame of that, and the past four months of going through old files while helping Coulson had brought her no new leads on who (or what) she really was. Skye felt like a time bomb, slowly ticking down until her powers would reveal themselves and destroy everyone around her in some way. She'd told Leo this one night when she woke up screaming from a nightmare where her powers caused a massive explosion and killed everyone she ever cared about. To her surprise, he'd taken it incredibly well, and agreed to keep it a secret from Simmons, Tripp, and Billy Koenig.

"So what's on the agenda today?" Leo asked, interrupting her thoughts.

Skye took a swig of her water bottle. "Well, Coulson's got me going through those files we got from one of the Academies to find out what we can use in the new SHIELD," she rolled her eyes. "Honestly, I don't know why I have to look through Academy files on cadets who were there in the sixties. I mean, I get it, look for the ones we know are Hydra, find what they did later, blah blah blah. But there's just so much stuff."

"You're all too capable of doing it Skye," Leo said, giving her a reassuring smile. "Trust me, I know. You're my best friend. It'll go fine."

_Best friend._ Skye blushed. "Best friend?" she asked, raising an eyebrow. "What about your science twin? You know, Simmons. The biochemist. Our friend who can't lie to save her life."

He sighed and ran a hand through his sweaty curls. "Simmons is…complicated."

Skye sat down on the bench. "Complicated?"

"Uh-huh," Leo looked shyer all of the sudden. "Don't get me wrong, she's been with me since we both started at the Academy and we're really close friends."

"And you got together too," Skye added, sounding a little harder than she intended. "Sorry, go on."

"Yeah," Leo fiddled with his water bottle. "But after I told her how I felt, something seemed different about her when I woke up. Like she was just being with me so I could be happy. She was trying really hard, I could tell. But I didn't want to be with someone who had to be another person to make me happy. Does that make any sense?"

Skye nodded. It made a lot of sense, and it brought back a lot of memories. Memories she didn't like to think about. "I get you," she said, avoiding his gaze. "That's why you split. Because you felt she was being the person you wanted her to be, and not herself."

"Mm-hm," he mumbled. "I told her this. She said she understood what I was saying. But she's still not the same Simmons I gave that last burst of oxygen to. She's changed. We still work great together and everything, but there's something different about her. She's quieter, more than usual. There's times when she hides whatever she's working on and when I ask her, she tells me what it is and I know she's telling me the truth because she can't lie to save her life, but it's like she's hiding things. Sometimes, I feel like she's watching me, and I'm not-"

"Leo," Skye placed her hand over his. It was warm and firm. "You and Simmons went through a traumatic experience, and that can change you. She probably isn't the same person you were with at the bottom of the ocean, but you aren't either. People change, and there's not a lot that can be done about it. But we can get to know the new person they are, and maybe even bring back the old one too."

He looked up and smiled at her. "You always know what to say," he said, wrapping his arms around her in a hug.

Skye almost melted in his warm embrace, but wrinkled her nose. "Ugh, Leo, you're great and everything, but you really have to shower. You smell so bad." She pulled away, plugging her nose and waving her hand in front of her. Leo laughed and walked off toward the door.

"Just give Simmons time, okay?" Skye said to him. "She was really worried about you when you were in the coma. She still worries."

Leo nodded and left. When the door slammed shut, Skye set down her water bottle and began to put away the mats, thinking about what Leo said.

There was something off about Simmons these days, and it felt odd. After everything that had happened with Hydra and Garrett and Ward, it was understandable that she could be more closed off and worried. But it felt like there was something more forced about her attitude now. As if she was trying to play a role.

"I'm being paranoid," Skye said aloud to herself, shaking her head. She knew Simmons; they all did. She couldn't hide anything from them, it was just impossible for her.

* * *

**If you think that Fitz woke up on his own, then Coulson was only dead eight seconds. Muhahaha.**

**Sooo what do you all think? And who wants to see Ward in this?**


	3. Chapter 3

**It makes me so unbelievably gleeful when I see how much people like this. Thanks for keeping up the support. It means a lot.**

**A few of you have already developed a theory about Raina and Skye. While I refuse to say anything on that, I do promise that more of Raina's reasons for protecting Skye will come about soon. It might come as surprise to some.**

**But first, how about a little Dark Jemma. (I love calling her that. It sounds so awesome!)**

* * *

Chapter 2: A Debt to Pay

_Three months ago_

_She sighed as she stared at the figure in the hospital bed. For over a month now, Fitz had been in a coma, and Jemma was getting worried more every day. She didn't need to act in front of the team when this was concerned. Her frustration and fears were all too real to be hidden._

_Jemma walked over to his bedside and took his limp hand in her own. "I'm going to fix you, Fitz," she whispered to the comatose engineer. "You're my best friend, and I don't let debts go unpaid."_

_With that she walked out of the room and back to the Playground's lab. Sitting on a stool was her contact, who had come in with a group of loyal SHIELD agents taking in supplies to the base. SHIELD's blatant naivety to anything traitorous going on behind their backs made her laugh sometimes. Coulson was hoping that the SHIELD he was rebuilding would be immune to that, but it was already too late. There were new seeds that she was planting within the new SHIELD. Seeds that would one day rise to bring out about the new age._

"_What do you have for me?" she asked coolly as she walked over to him._

_The contact smiled. "Darwin received your gift and heard of your plight," he said, reaching into the pocket of his jacket and pulling out a plastic case. He handed it to Jemma. Through the lid, she could see a syringe, filled with a blue-tinted liquid. "He thought that this would be proper payment."_

"_What is this?" She was puzzled. "If this is for what I reported to you on Director Coulson, then I'm sorry to say that he already gave me help. There have been no more incidents in connection to the GH-325. The serum I made with the help of Darwin's notes stopped the effects, and he's received copies he wanted of the writing that the director had been making."_

"_This is for the engineer." Her contact stated. "Darwin heard of what he did for you."_

_Jemma pursed her lips as she remembered the last few minutes that she had spent down in the med-pod. Fitz had practically told her he loved her before pushing that button and leaving an enormous debt behind. She might not have feelings for him like he did for her, but she never let debts go unpaid._

"_Is this the serum?" She asked suspiciously._

_Her contact shook his head. "They don't know what it does to coma patients, and if it has a serious effect on them…"_

_His voice trailed off into uneasy silence. Jemma knew that Darwin's serum could do wonderful things, but there was also the possibility that it could make you into a literal monster. She'd seen the latter effect plenty of times before, and shuddered at the thought of it happening to Fitz. "So what will it do?"_

"_This is__ going to wake him up." Her contact got to his feet. "Darwin had interest in him as an asset. He wants him to join us. You have power over him, and he believes you can convince him to join us in the making of the new age."_

_Jemma's lips pulled upward into a smile. She might only see Fitz as her best friend, but clearly he felt more for her. Those feelings could be milked to bring him closer to Darwin and his plans of a new age. If he was reluctant, she could cite that Darwin had helped save his life, and that he owed them that. But she knew Fitz was loyal to her, and would follow her to the ends of the earth if necessary._

"_Tell him I said thank you," Jemma told the man as he walked toward the lab doors. "Are you going back to him now?"_

_Her contact shook his head. "After I get back to a base with the rest of the bozos, I'm on my way to visit a prison. Darwin wants me to have a chat with the guy responsible for you almost dying."_

_Ward. Jemma felt her fists clench. "Why would Darwin care about some low-level Hydra agent?"_

_The man merely chuckled. "He said that if someone tries to take out one of his operatives, then they need to learn a lesson about messing with us."_

_With that, her contact slipped out the door to meet up with the rest of the supply crew._

_Jemma walked back to the hospital wing and stared at Fitz's almost still form. She opened the box with the syringe. After sterilizing the patch of skin, she injected the contents into him. Once it was done, she placed the syringe back in the box. She'd dispose of it as soon as she could later. _

_She smiled when a slowly growing spike appeared on the screen monitoring Fitz's brain activity._

* * *

_Present Day_

Her phone began to buzz just as she took out Fitz's file to update it. She'd been noting his behavior carefully each day ever since he woke up from the coma to see if any side effects from Darwin's serum. Thankfully, nothing had occurred yet, unless the changes in his attitude toward physical training could be counted, but she highly doubted that. Still, Jemma preferred to be cautious, and watched him carefully whenever he was around her.

Sighing, she pulled out the phone. The caller ID read MUM AND DAD, and she looked about anxiously. When she was satisfied that no one was nearby, she pressed the answer button, smiling to herself. Everyone always thought that she was speaking with her parents whenever they saw the caller ID, but it never was. Her parents had been divorced for six years, and each had their own personal mobile number that they called her on. However, one of Darwin's higher-ups had toyed with some files so it had appeared on her SHIELD documentation that her parents were still married.

"Hello."

"Agent Simmons."

Jemma stiffened at the recognition of the voice. "Yes."

"Are you in a position to speak freely?"

She looked around her again, and pulled the phone away from her ear to listen for any approaching nose. "All clear."

"Excellent." She could practically hear him smiling. "I've got some news for you."

Jemma leaned against the lab table, listening closely.

"It's time for you to bring in the girl. I think my reunion with her is long overdue, and I don't wish to postpone it any longer. And the engineer should be brought along as well."

"Fitz?" Jemma was puzzled. "Why would you want him? He doesn't have the serum running through his veins. What purpose do you have for him?"

"Neither do you yet, but that doesn't mean he's entirely useless. The formula that is responsible for his recovery…have you managed to get a blood sample yet?"

"No," Jemma replied with a sigh. When Skye had been injected with the GH-325, it had been all too easy to get blood from her to send to Darwin's base. Fitz, on the other hand, presented more of a problem. There was no way to take a blood sample from him without arising suspicion. She might be one of the best liars out there, but even she had her limits.

"We want to run some more tests with it. There is the possibility that it can reverse some of the more negative outcomes of the serum and turn them into positive ones."

She closed her eyes and smiled at the thought of Fitz helping her out in one of Darwin's labs, working to reverse the nastier side effects of the serum. Raina would be there too, and Skye could drop by and visit them. It was a lovely thought. They could all be together as the new age dawned upon humanity.

"Are you sending in an extraction squad for just them," she asked. "Or will I be the one taking them to you?"

A soft chuckle drifted into her ear. "A bit of both, Agent Simmons. I'll keep you posted on updates, but I'm very sure that you'll be back in one of our labs quite soon."

The line went dead, and Jemma stuck the phone back in her pocket. She remembered how much she had enjoyed acting as a child. The process of slipping into another role, becoming a new person was utterly fascinating. It had been a passion that rivaled with science, but she balanced the two easily. In fact, she had planned a back-up career as an actress if her primary plans of becoming a biochemist fell through. Luckily for her, they didn't. But fate had still allowed her to combine her two of her passions into one job.

Infiltrating SHIELD had been no easy feat, and the mask of sweet and innocent Dr. Jemma Simmons, who liked Doctor Who and pistachio ice cream and could not lie to save her life, had been in place for a long time. She'd been careful, but sometimes the mask would begin to fuse with her real self and she got too close to people. Fitz was the prime example of it. Luckily, she could only see him as a friend and nothing more. The fact that his feelings had once differed had led to a month-long role of masquerading as his girlfriend, and it hadn't been a role she'd enjoyed very much. Thankfully, she still had his trust, which was what she needed most.

Muffled voices could be heard getting louder, and Jemma scurried to put away her notes on Fitz's recovery. As Fitz and Skye entered the lab, asking her how her morning had gone, she pulled on a smile and answered their questions in a bubbly tone. To herself, she imagined a different scene, where they were all in another lab, a much more sophisticated one, with another person.

"_We'll be together." _Jemma thought to herself as Skye asked her to speak in 'simpler English' about a new dentrotoxin. _"It'll be great. You might not see it now, but as soon as you open your eyes, you will see the wonders you've missed."_

She couldn't wait to be out of this place. It would feel all too relieving to pull of the mask of cheery smiles and go back to being the real Jemma Simmons.

**Oooo what's going to go down? You'll find out….**

**And yes, the baddie's name is Darwin. It's not his real name though, just something he likes to call himself. You'll understand why later.**

**Please leave a review. Tell me your thoughts so far, and tell me which is a better name- Yu or Hua? (They both have meanings.)**


	4. Chapter 4

**Ehehehe I'm in a really good mood right now. We've got less than a month of agonizing wait until season 2 comes out. I hope that I'll like Lance Hunter, because I might be including him in the story.**

**(And if I'm completely honest, I wouldn't be entirely angry if Jemma became a bit of a villain. I really, really love Dark Jemma. I mean, I can practically see this stuff going down as I write. Should I be worried about that?)**

**In this chapter, you're going to see something interesting in Leo's thoughts. The story behind it is kind of my personal headcannon for his past, and the full story will be revealed in later chapters.**

* * *

Chapter 3: There Was No Shot

"_She'll be safe." The man in the white lab coat looked down at the small baby in the messily wrapped white bundle._

_She swallowed. "Promise?"_

_He looked up at her, but it was Darwin's face. In his arms, Tian Kong was gone, and replaced by Skye. The girl's body was limp and lifeless with claw marks and blood covering her entirely._

"_Of course," he sneered as she began to scream._

Raina's eyes snapped open. It was just a dream, but seeing Skye's body like that made her shiver. She'd witnessed Darwin do that to people in person before, but it had been while she didn't remember the other things. Now, she avoided it and him, at all costs.

Clutching her sheets, Raina tried to calm herself down by taking deep breathes. The moonlight streaming in from her window illuminated her small chest of drawers. On it, she had painted some of the flowers she remembered from the garden of one of her clearer memories. They had been times where things were happier, or at least she hoped they were.

"_Please,"_ she thought. "_Please don't let them find her. Please let her be safe."_

* * *

"It's time." The gravelly voice filtering through the phone said. "You know what you must do."

Jemma allowed herself a dark smile. "Of course."

"Excellent."

The call disconnected, and Jemma put the phone in her pocket. She grabbed the collapsible baton, red dye, and the wire cutters. Satisfied, she slipped out of her bunk, and walked toward Koenig's office.

* * *

"This had better be worth my time, Leo," Skye announced as she entered the rec room with a bowl of popcorn. "We've only got a few hours until Coulson, May, and Trip get back with the new people, and I really need to not slack off on finishing uploading the database for the Index."

Leo snorted. "It's worth it, trust me," he assured her as he slid the disc into the DVD player. "You are going to fall in love with this."

Skye raised her eyebrow. "You seem quite sure of yourself."

He flopped on the couch beside her. "Of course I am," he smiled at her as the swirling blue lights and police box appeared on the screen. "Doctor Who is a classic, Skye. It has everything in it! I can't believe you haven't seen it yet."

"Well, sorree." She pitched a bit of popcorn at him, which he threw back. "Did you watch this with Simmons at the Academy?"

Leo sighed and nodded as the first episode began to play. He'd offered for Simmons to come and join him in educating Skye in great British television. She's turned it down, explaining that she had work to do. During the conversation, she'd been very fidgety, as if she was waiting for something to happen.

The thing was, she had become even more distant recently, and it bugged Leo. He'd begun to notice it more in the past week, after his conversation about her with Skye. There was a colder tone to her voice when she spoke, and she was more secretive about the projects she was currently working on. She had also been taking a lot more calls from her parents recently. But Skye had only just managed to rebuild them again thanks to a back-up hard drive and Agent Hill finally managing to get SHIELD cleared of all charges filed against them. Simmons's parents were probably just catching up with her after the four to five months spent off the grid.

Everything that seemed odd about Simmons could have an easy explanation, but Leo couldn't shake the feeling that something was off. He was being paranoid, he knew that. Still….

"Uh, Leo?"

Skye was clutching a pillow close to her chest as she watched Rose Tyler flee from the plastic mannequins of death. "This is kind of creepy. Shouldn't Doctor Who come be with her?"

"It's just the Doctor, Skye," he reassured her, hiding his grin. "And be patient."

The mannequins were about to grab Rose. Skye was holding her breath in anticipation, while Leo waited in glee to see how she would react to Christopher Eccelston.

Then the lights went out.

* * *

Jemma stood up and replaced the wire cutters back in her pocket. All of the Playground's generators were completely useless, except for the one that she couldn't completely ruin, so she set it on a timer. They had an hour to carry out their mission in the orange glow of the exit emergency lights.

She looked at the leader of the extraction squad. "Send two of your most expendable men after me thirty seconds after that door closes. The rest of you wait here until I call you."

She pointed to the door leaving the generator room, then pulled the vial of red dye out of her pocket, uncapping it.

"Wouldn't it be easier to send all of us?"

Jemma silently wished for more light so the idiot could see her rolling her eyes. "They may not seem so, but these two are tough. To take them out, they must be worn down first."

* * *

"Isn't there supposed to be a back-up generator or something?" Skye asked nervously after clicking on the flashlight he had just handed her. "I mean, it's a SHIELD base. They probably have a back-up. Why isn't it working?"

"I don't know," Leo admitted honestly. Last month, he'd checked all of the generators out, and they'd been fine. "Something must have happened to all of them."

"Like what?"

Leo was about to reply when the sound of distant running hit his ears. Signaling Skye to shut off her light, he flicked his off as well. The emergency lights in the hall bathed her face in a creepy shade of orange.

"No, no, no, no" a terrified voice pleaded. "SOMEBODY! HELP ME!"  
Leo looked over in Skye's general direction. "Simmons," they said together.

They managed to maneuver their way around toward the door without a problem. On his way past the pool table, he grabbed one of the sturdier cues. Trip had told him that just about anything could be used as a weapon. Leo already had a pocket knife, but preferred a bit of extra insurance. Odds were that the intruders had guns, the thing that Leo despised more than anything in the world. ICERs couldn't kill, but guns…

_A single shot. The limp form. Red, green, blue, grey, and copper. _ He shook his head, ridding himself of the horrible memory.

Peering out into the hallway, they saw Simmons stumbling toward them, clutching her side. In the eerie orange glow, Leo could see her hands were stained with something dark. She'd been shot, but by who?

His answer came a moment later when two goons, carrying rifles rounded the corner, and advanced toward Simmons, who had fallen just inches from the doorframe, in the middle of the hallway.

He felt Skye move past him, and watched as she jumped out in the open. Her flashlight flew out of her hand and slammed just below the visor of one of the goons. He dropped his gun and fell on his knees, groaning. The other turned his attention to where Leo and Skye were now visiable, and raised his rifle. Leo dove and pulled himself and Skye to the ground as a burst of gunfire passed overhead.

Getting up, Leo charged at the shooter, while Skye made her way over to the other goon who was now getting up. Spinning the cue, Leo knocked the gun out of the enemy's hands, then swept his feet out from underneath him. Unfortunately, the cue snapped in two. Still, Leo was able to grab the gun, and slammed the butt of it against the helmet. The guy dropped like a stone, but he was still breathing.

Skye had dispatched the other goon a bit faster, and was now at Simmons's side. As soon as he saw the blood, Leo turned away.

"I saw them," Simmons was hysterical, and was keeping her hands overtop her wound. "I heard noises from Koenig's office, and when I went in, he was on the floor with them over top of him. I screamed and ran, and then- then they shot me!"

"You're okay now, Simmons," Skye soothed, easing the hands away. "Let me look."

Leo cringed a bit at the wall. He hated to see people bleed, especially those who he was close too.

_Blue sky. Red barn. Birds chirping. Then the gunshot, shattering the peace. The total si- Wait a moment!_

Leo tuned out Simmons's whimpers and retreated into the library that was his brain. Simmons had been shot, that's what she had told them. Bullets come from guns, and a gunshot is heard when the trigger is pulled and the gun is fired. Unless, of course, you happen to have a silencer.

The guns at his feet had no silencers.

Since the power went out, there had been not a single sound except for Simmons's scream.

They should have heard a gunshot. They didn't. That meant that Simmons….

A _thud_ and the following groan brought him back to reality.

Leo turned around slowly, feeling his blood go colder by the second. Simmons was standing over Skye's limp body, a collapsible baton in hand. Her hands, which once looked wet with blood, had now dried into something lighter, and he couldn't see any more flowing. The way she held herself disturbed him. This woman before him was not the one who had befriended him at the Academy. She wasn't the one who dragged him into making the best decision of his life. She wasn't the Simmons he'd given the last breath of air to. She wasn't the Simmons he knew.

"Simmons," he breathed, stepping back. "Why- what are you doing?"

The woman before him sighed and looked up at him with…..sympathy?!

"Oh, Fitz," she sighed, as though preparing to lecture him. "It wasn't supposed to happen like this."

She advanced toward him.

"Stop this, you're scaring me."

She gave a chilling laugh. "Oh, I've missed being able to do that. It can get _awful_ tiring, pretending to be nice and sweet all the time."

Her smile dropped. "I'm sorry for this, Leo," she whispered. "But you'll soon understand."

Something hit his temple, and he fell to the ground, right next to Skye as his world turned to darkness.

* * *

***creepy smile* So do you guys understand the title now? If you saw it, of course.**

**So, between Hua (flower) and Yu (rain), which is a better name for a female character?**


	5. Chapter 5

**Season 2 has dawned upon us, agents, and right now it hurts like heck. I cry for my poor Scottish Science monkey-prince, but now after that promo for episode 3….ehehe I might be a little too happy now because my treasured Skitz might have a chance. Both got seriously injured, both have someone they love leave them, and I now desire it much more. *cue muse screaming 'BAD MARY!'***

**But in all honesty- Jemma WTH!**

**Um, yeah this is pretty much AU now because I wrote this before the premiere, and I still own nothing besides this crazy idea. The flashback in here is told from Raina's perspective too.**

* * *

Chapter 4: Things I have lost

Billy Koenig blinked his eyes open, wincing at the throbbing in the back of his head. It ached horribly and for some reason, he was on the floor. The last thing he remembered was turning at the sound of the door opening, and then something striking him in the back of his head. Shuddering, he thought about how lucky he'd been that the person who had hit him hadn't killed him. If only Eric had been that lucky with that Ward guy.

Billy had been very private when it came to mourning his brother, which had come as an enormous shock to him. He'd thought that being in charge of Fury's secret bases was pretty much a safety guarantee after Hydra rose up. Hearing that Eric was dead was one thing, but people thinking that he was him was another. Sure, they were identical twins who pretty much shared a brain (or at least, they had). Still, it hurt that they couldn't see him past his brother.

Climbing back up to his feet, Billy frowned as he noticed the monitors that were supposed to be playing security footage now displayed static. He huffed in annoyance. It was probably the work of that hacker girl, Skye, and her friend Agent Fitz. The two were practically peas in a pod and full of mischief. Both of them loved to play practical jokes on him a lot, but he wasn't falling for this one.

Billy reached into his desk drawer to grab his air horn that he had reserved just for them and walked out into the hall. As he strode down the halls, he noticed that some of the lights were only now just flickering on. Billy frowned. _If those two had been playing with the lights…_

"Agent Fitz? Agent Skye?" He called as he rounded the corner to the recreation room. The engineer and told him that he was going to show Skye Doctor Who. Apparently, the poor girl had never seen it before, and Agent Fitz was taking it upon himself to rectify that mistake. However, he couldn't hear any sounds coming from the rec room, or even from the two younger agents.

Now he felt worried, but maybe they were down in the lab with that biochemist. Billy pulled his radio out. "Agent Simmons? Are you there?"

He was meet with static, and decided that it would probably be best if he went down and checked in on them. Just as he took a step forward though, his foot skidded over something. Catching his balance in enough time, Billy leaned down.

It was a pool cue-_his pool cue!-_ broken in two jagged halves. Billy inhaled sharply and looked around him. A few steps from him was a flashlight with a crack running through the lens. It was lying next to a dry red splotch that he knew had not been there the last time he passed through the hallway.

Something was indeed off here, and he didn't like it. Agents Fitz and Skye weren't that patient enough to stay and let him fret for this long, and Agent Simmons was always punctual in responding. Swallowing, Billy pulled out his phone and pressed in the Director's number.

* * *

"Hello?"

"Director Coulson," Billy Koenig's voice sounded tight with worry. "Where are you at right now?"

"Hold on a sec."

Phil turned in the co-pilot's seat to look at Melinda. "How far away-"

"An hour at the most from base," she answered instantly before frowning. "Why?"

"Koenig, we're an hour out," Phil replied, pressing the speakerphone button. "Is everything fine at your end?"

There was a long pause. Phil looked over at Melinda. Her eyes filled with concern as the silence dragged on.

"Koenig?"

"Something happened here," Koenig's voice was quiet. "But you need to get back here as soon as you can. I'll fill you in then."

"What's happened?" Melinda asked worriedly.

"Agents Fitz, Skye, and Simmons…they're gone."

The Bus jolted a bit as Melinda flinched at the mention of Skye's name. Her face was now deathly white, and fear radiated off her in waves. It was a fear that Phil hadn't seen her in since Bahrain.

"Melinda?" he asked as she began to take deep breathes. She'd done this before, after Bahrain had happened, to ward off panic attacks. "Melinda?!"

She relaxed and swallowed. "I'll get us back as soon as possible," she whispered. "Could you please leave?"

"Melinda, are you okay?"

"Just. Leave." She flicked some switches and turned away from him, her eyes on the horizon.

Phil nodded and left the cockpit, knowing better than to press her for further information. He understood that Melinda cared for Skye like a daughter, and was quite protective of her since she'd begun to train her. She was doing so much for the hacker, and doing everything she could to prevent Skye from having her own Bahrain. But right now, after seeing Melinda react, Phil was concerned that she was about to walk into another.

* * *

_What will I become?_

Raina was lying on her back over her bed, staring up at the ceiling. She remembered asking Garrett the question, holding back the one she really wanted to ask. The one she wanted to know about most of all. The one she had needed to know about since the day she remembered.

_Who am I?_

For most of her life, she thought everything was perfect. It was just her and her father, moving from place to place around the world so he could perform his work, which he had told her was to make people better. Throughout her childhood, she'd seen the wonders he'd gifted to people through his work and marveled over them. There had been numerous times where she'd see water fly in spirals with a flick of someone's wrist or a blur of a person shoot down a football field in less than five seconds. When she told her father about the 'special people', he would chuckle. "You're like them too," he would say.

"Nuh-uh," she had told him. "I can't do anything."

"Maybe one day, you will." That reply made her shudder now, knowing what he had done.

At seventeen, she had decided to study chemistry, and had found herself under the tutelage of a professor who worked closely with her father. After that, she moved into biology, anatomy, zoology. She soaked up scientific knowledge like a sponge, and soon found herself working on her father's serums that he used to 'heal' people.

When she was eighteen and pursuing the zoology field, she met another girl around her age. She was the first person from the outside world who hadn't been living in one of the facilities that her father managed. The girl, who her father called one of his finest pupils, helped her out in the labs often, and worked well with Raina.

Her name was Jemma Simmons.

Simmons was a great friend who had a passion for science that Raina understood. However, Simmons would only be there a few weeks at a time, disappear for months, and then return again. Her father told her that she had work elsewhere and was helping gather information for him. When she begged to go along with Simmons once so she could see the outside world, meet other people who loved science, her father turned down the request and ordered her to stay. While she meekly obeyed, the desire to go out in the world beyond her father's domain was overwhelming.

The minute an opportunity to investigate the possibility of a clairvoyant, as well as a serum that could give people increased strength, came up, she pleaded to be the one to go in, and her father had agreed reluctantly. He told her to be careful and to not get in too deep. Raina agreed, but secretly planned to investigate the many questions she needed answers to.

Despite her seemingly perfect life, there were things that always bothered her. For example, she knew nothing about her mother. Her father had told her that she had left them while she was an infant, and died a while later. But the explanation never seemed right to her, and she constantly questioned if he was hiding something from her.

Then there were the odd gaps in her memory where it felt like white space, the largest ending at her fifth birthday. While the others occurred here and there, this one bugged her the most. It didn't feel natural, as though she was forced to forget.

It was with Centipede that she discovered the truth. She'd played along with them, acting loyal on the surface while later hiding in closets trying not to cry over seeing the horrific loss of human life. Watching a person meltdown like that made her feel so glad that her father's serums never turned people into monsters. Or at least, she had felt that way before she remembered.

It was because of the machine they used on Coulson that she remembered. The inventor had bragged about its capabilities, and Raina couldn't resist herself in challenging them. At first, the inventor was reluctant, but eventually she was persuaded into testing it out to see if it could fill the blank spots in Raina's memory.

That was the last time Raina ever felt truly innocent.

The machine had hurt, but what she saw in the places she had forgotten hurt her more. She saw that her father's serum failed more often than the Centipede serum, more often that she had even thought possible. It could give people incredible skills, yes. But it also mutated people into horrific monsters. Those times had filled her with fear, and her father had wiped her memory with a machine so she would never doubt him. It made her sick to see all of it, but she had to get through it to see further into her past.

Unfortunately, the machine suddenly stopped when she hit a memory of her mother around the age of four. One memory of the woman who gave birth to her, and then there was no more. Shaking with fear, she got out and saw the woman who had made this life-changing device slumped over the control panel, crimson staining the controls from her slit throat. Horrified, Raina had run over to the trash can and vomited.

When Raina returned to her father's base, everything around her was suddenly horrific and grotesque, but she put on a mask and pretended like everything was normal. She began to notice more, and searched for more answers. She confronted her father about erasing her memories, which he denied. But she knew he was lying to her, and decided to take matters into her own hands.

Two nights after she first arrived, she broke into the room of files and pulled out hers. Sitting on the floor at night, she read what wasn't blacked out and learned that for her entire life, she had been nothing more than an experiment on human evolution. It was in that moment that she vowed that she was going to stop her father, if she could even call him anymore. In fact, she stopped calling him that in general and referred to him by the name he was known to his followers (or cult as she now called it).

If she had not seen two particular memories, then she would have left a long time ago. But it was because of something she'd confronted her father about for never telling her that she stayed. She stayed to stop that horrible man from achieving his goal. She stayed because her mother was most likely dead, and there was no one out there to keep her safe. She stayed to sabotage any effort Darwin made to find her.

She stayed because she had to protect her little sister, whoever she was…

* * *

"_Mama?"_

_Her four year old self toddled outside and down the front steps. A wide smile crossed her face when she saw the figure that she knew was her mother bent over a bunch of bushes with flowers on them. Her little legs flew down the path toward her mother. "Mama!"_

"_Hua."_

_Her mother's arms tightened around her. "Where have you been at?"_

"_Jus' playin'," she answered. That's what Daddy always told her to say when he gave her the 'in-yec-tion' as he called it._

_Her little sharp eyes gazed out on the garden, which was full of blossoming flowers. "Do you like flowers, Mama?"_

_While her mother's face was fuzzy from the memory wipe, her smile was still radiant. "Of course, sweetheart. Who doesn't like flowers, Hua? After all, you're my little fower."_

_Smiling, she scooted closer to her mother. Something bumped against her cheek, and she giggled._

"_Baby?" she asked, pointing to her mother's round belly._

"_Uh-huh," her mother replied, rubbing it a little. "Your little sister is saying hello."_

_She blinked, awestruck. "Sister?"_

"_Yes, Hua. You're going to have a little sister soon," her mother kissed the top of her head. "Do you want to hear her name?"_

_She nodded._ "_Yeah."_

_Her mother leaned over. "Tian Kong."_

"_Shi-an Kon," she whispered, delighted as she sounded out the pronunication. "Hua and Shi-an Kon."_

_Her mother laughed. "My little flower, and my precious sky," she murmured softly._

* * *

**So yup, there's my theory on Raina/Hua and Skye/Tian Kong. Did I surprise anyone or did people suspect this? **

**Please leave a review and tell me what you think of this. I am also available for anyone needing consolation regarding the whole Jemma is you-know-what thing.**


	6. Chapter 6

**Yet another chapter of this has arrived, and I hope you're all excited for it! I'm so thankful for all those who have been reading, favoriting, following, and reviewing for this story. It means so much to me whenever I see a new follower or review, because it means that people are reading and enjoying this!**

**So I'm guessing there's a great deal of you who were pretty stunned by the revelation last chapter, and I hope it hasn't turned any of you away. While Raina isn't in this chapter, she will be very prominent later on with Fitz and Skye in later chapters.**

**Leo and Skye were originally going to be in this chapter, but looking back I saw it was waaaay too long. It was also pretty rough emotionally as Skye found out about Jemma, but I have it down and will it up soon! But for now, enjoy!**

* * *

Chapter 5: The Empty Bedroom

_24 years ago_

_Something was off in the house, and it wasn't just the lights. From where she stood at the front steps, her home looked unusually empty without any lights or sound. Normally, she would come home to see Hua pressed against the window or Tian Kong screaming in happiness or hunger. Even Edwin was usually up when she came home, no matter the hour, working._

_Working in his lab._

_Suddenly, she stopped. The groceries she'd picked up on her way home from base crashed to the sidewalk. Panic gripped her heart as she remembered what she had found the week before in her husband's lab. Those plans, the charts, the equations. The two files showing what he had done to their two most precious, darling children. Had he found out she was planning to take Hua and Tian Kong and run?_

_Trembling hands forced the key into the lock, and she pushed the door open as soon as the tumblers clicked. Racing up the stairs, she flung open Hua's door. The sight of the empty bed sent her screaming, and she stumbled out of the room, down the hall to Tian Kong's nursery. Hua loved her baby sister, and she often had to drag her daughter from the room so her younger daughter could get some sleep._

_The moment she saw the empty crib, she collapsed beside it, screaming and wailing until her voice was nothing._

* * *

_Present Day_

"Play it again."

"You'll find nothing new," Melinda muttered. They'd been back at the base for a couple hours now, and they had found no leads "We've seen it over and over again. The squad just pulls up to the door nearest to the generators, and then everything goes dead. There's nothing there, Phil."

"She's right," Koenig told Coulson, who gave him a stony look. "Whoever did this was good, and quick."

Tripp nodded from his position against the desk in Coulson's office. "They broke in, cut the power, knocked you out, and then made off with Skye, Fitz, and Simmons. Now Simmons, I could understand if it was just her. No offense to her, but she'd got little field experience and training. But Fitz and Skye….May you've seen them spar with me before. They're tough enough on their own, but together it would take something pretty powerful to overpower them."

"Wait, Fitz? I know that name," Agent Blake frowned and shook his head in bewilderment. They'd picked him up with a small group of mercenaries whose leader, Isabelle Hartley, was an old buddy of theirs. "Not that scrawny kid who lives in the lab, right?"

"Agent Fitz has changed his views on field work these days," Coulson said defensively, glaring at Blake. "He's quickly rising to become one of our best."

"Must have taken something big. That kid was practically superglued to the lab," Blake muttered under his breath. Tripp shot him a dirty look.

"Getting dropped to the bottom of the ocean and falling into a two month coma changes you," Coulson shot back.

"Like getting shish-kebabed by an Asgardian nut case?"

"That's something coming from the guy who got stomped on by-"

"ENOUGH!" Melinda screamed, jumping up. She was tired of hearing everyone banter uselessly. Skye was out there, probably in serious danger. "All of you, just stop it!"

Everyone fell silent, staring at her. Melinda could understand why. Her outburst was uncharacteristic for the normal stoic image they all held of her.

"Look," she said tightly. "I know that this is not what we expected to come back to. I'll tell you this though. If we want to find out where the hell they are, then we need to stop re-watching tapes and arguing because of personal grudges. We need to stop and just think this out."

Melina swallowed thickly, holding back the searing pain that had ripped through her when they first got back to the Playground. "Does anybody have any idea how they got in?"

"Hydra."

Everyone turned toward Tripp, who was looking at Coulson. He nodded at Fitz's S.O., prompting him to continue.

"Look, Hydra's our number one enemy, right?" Everyone nodded. "They've got SHIELD tech from the uprising, and there's bound to be stuff that they can use to break into wherever they want to get to."

"But the Playground's enormous," Billy exclaimed, spreading his hands out to imply the vastness of the base. "My first week here, I got so unbelievably lost! It took an hour to find my office once so I could find the map to this place. There's no way a troop of that size could have gotten up here in that amount of time."

"Unless they knew where they were going," Tripp said, looking at her and Coulson. "We found our way around pretty quick. The layout here, it's exactly like the Providence base. Hydra had a man who was at Providence. He also stayed here for a few days in a holding cell before he got transferred to a prison."

"You're not talking about who I think you are, are you?" Melinda whispered, feeling a wave of cold wash down her back.

"He has zero contact with anyone other than those who are authorized to be with him," Coulson pointed out. "How could he even tell someone this?"

"He could have given it up before we got him," Tripp suggested. "Or someone else from Hydra snuck in and got it from him."

"And passed it onto that squad!" Koenig finished excitedly.

"So we have something, now what?" Blake looked over at Coulson.

Melinda met his eyes and nodded. Coulson sighed and turned back toward the rest of the group.

"I think we need to have a visit with an old enemy."

* * *

"Did you succeed?"

Simmons nodded. "Of course, sir. They never saw it coming. Utterly clueless, the both of them."

"And you made sure the message was left behind."

"I did."

"Do you think the others will suspect you?"

Simmons shook her head. "They trust me completely. Getting dropped into an ocean by a member of Hydra solidified their faith in me. Most likely they'll blame Hydra for taking them."

Darwin smiled. "Excellent work, Agent Simmons," he said approvingly. "I knew you could get the job done."

"So what happens to next?" his follower asked.

Darwin leaned back in his chair. It had been twenty four years for his desire to reach completion. Now, he could finally enact his solution with his daughter back. He could mold her to see things as he did, as those loyal to him did. He would succeed where he failed with the other one.

"I think," he mused thoughtfully, rubbing at a bloodstain on his white coat. "It's time to see my little girl again. Bring her up to meet me, Simmons."

* * *

**Oooo what's going to happen? You'll find out!**

**There's a poll on my profile regarding Ward in this story. I can't decide where to take him, because either direction would be great. If you would be super awesome to go by and vote, then that would be great!**

**Please leave a review. Your comments provide me with a big positivity boast when I write! Also, should the story title be changed to 'Hidden Secrets'?**


	7. Chapter 7

**Wowza! This has gotten almost a thousand views since I last updated! I've never seen so many followers yet! This is fantastic, thank you all so much!**

**Also, regarding the poll on my profile for the fate of one Grant Douglas Ward, I'm informing you all that at this moment that an alliance with the team is currently beating one with Jemma. There's still plenty of time to vote on his choice, so feel free to stop by and cast a vote!**

**So I decided to change the title of this to 'Hidden Secrets' because 'The Photograph isn't really fitting anymore. Also, this is so AU now due to all the things that have happened so far this season. Oh, and speaking of this season, I do plan to include Hartley, Hunter, Idaho in the story later on, as well as Bobbi and Mack. (thank you **_**agents-of-frickle-frackle **_**for cementing my love for Idaho before the show began, and then promptly ruining me in the first episode. You're awesome!)**

**Also, there's about three Doctor Who references in here, and one of them is a Ten saying. (Not Allons-y though, another one)**

**This chapter…I don't even know how to explain it other than I hope I don't hurt you too much. **

* * *

Chapter 6: The Truth Hurts

Leo winced as he cracked his eyes open. There was a dull ache in the back of his head, but it was slowly fading away. Blinking his eyes fully open, he found himself staring up at a gray-green ceiling. To his knowledge, and he should know because he had been living in the place for four months, there was no room at the Playground that resembled this. Frowning, Leo turned his body to the right and rolled to the ground from a cot that he had been on. His hands connected with a cool cement floor as he looked around, confused.

He definitely was not in the Playground anymore, that much was certain. The room barely eight by eight feet for one, and then there was the heavy steel door. Leo got up and found it bore no handle to open. Sighing in frustration, he turned around to observe his surroundings behind him. Now he could see how sparsely furnished the room was. A barred, reinforced window was their only illumination, and aside from two buckets in two different corners (which, he was disappointed to learn, were bolted down), the only other items in the room were two cots. There was the one he had rolled off of, and another that was occupied by Skye.

Skye!

Leo rushed to her side, cursing himself for not thinking or noticing her earlier. He breathed a sigh of relief when he saw she was still breathing _'She's alive,'_ he thought, glad that she was with him. Skye was one of two people he trusted to have his back, the other being…..

Simmons. Leo froze and covered his mouth, remembering what had happened before he had woken up. He felt his legs buckling, and sat down against the wall by Skye, trying not to throw up.

_It wasn't supposed to happen like this._

_Oh, I've missed being able to do that. It can get awful tiring, pretending to be nice and sweet all the time._

_I'm sorry for this, Leo, but you'll soon understand._

She'd stood there like some terrible thing, bathed in those orange lights with a baton in hand and Skye at her feet. The cold gleam her eyes shone with as she came toward him. Her harsh laugh ripping away the image of the person who he had known her as. Leo knew Simmons had meant every word she uttered with malicious intentions. He thought she was sweet and innocent, absolutely incapable of doing anything this hideous. In reality, she was like a spider, weaving an invisible trap that he and Skye had helplessly fallen into.

When Hydra first reared its ugly head, Leo had been able to keep his world from falling apart to greatly because of Simmons and later Skye as well. Now, after seeing what he had, it felt as though a good chunk of it was crumbling to dust. He'd grown as a person thanks to his friendship with Simmons. Anything he'd ever known about her suddenly seemed flimsy, and Leo wondered if anything she ever told him was true. Her strange behavior in the last few days now made a lot more sense though. Her fidgetiness, the multiple calls, those small clever smiles that came out of nowhere for no reason, it all made sense now. Simmons had been plotting this for a while.

"Skye," Leo turned and gave her shoulder a small shake. "Skye?"

She twitched and groaned. "Whu?"

"Skye," Leo felt a bit of tension leave him when he heard her voice. "Wake up."

Her eyes fluttered open. "Leo?" Skye frowned, looking confused. "What's going on?"

"I'm not sure, only woke up a few minutes ago," he replied as she sat up. "Are you okay?"

"Yeah, yeah, 'cept I'd like to know where we are. Also, and I know this isn't a huge priority, where are my shoes?"

Leo cracked a grin as she stuck out her cat sock clad feet, and then down at his own socks. He hadn't realized that his shoes were missing until now. His watch was also gone, and the buttons on his shirt had been ripped off, leaving it hanging open to expose his undershirt. Clearly, someone was doing what they could to take away anything that they could use as a weapon or way to escape.

"I…don't know," he confessed when he realized Skye was waiting for an answer. "I don't know where we are, or what's happening, but something is definitely going on."

"Wait, Simmons!" Skye's head whipped from side to side as she scanned the room. "Where's Simmons? Leo, she was hurt, they shot her!"

Leo swallowed uncomfortably. Skye had no idea what Simmons had done, and he was going to have to tell her. "Skye…"

"Do you think she's alive?" whispered Skye, tears building up in her eyes. "We can't lose Simmons, Leo. She's like a sister to me. I can't lose my sister."

Leo clenched his teeth at the last sentence, feeling the painfully memories stir up.

"_I hate this. It's all my fault, Mum. He wanted me to drive, but I didn't feel like it and I told him I was tired."_

"_It's not your fault, Charlotte. You didn't know about the other driver."_

"_But it should have been me. I should have been the one. It's my fault Dad's gone!"_

"Leo?" Skye was waving her hand in front of his face. "Are you okay? Come back to me."

He met her eyes and gave her a nod. "Yeah," he lied, shoving the memories back down. "Skye, what's the last thing you remember?"

"I was trying to move Simmons's other hand out of the way," she said after thinking for a moment. "She'd gotten one of them out easy, but wouldn't budge the other. It was almost out of the way when something hit me in the head, and then I blacked out. Next thing I know, you're calling my name."

Leo took a deep breath to gather his courage. He had a terrible feeling that he was about to destroy Skye's world. "I know who hit you," he said, sitting beside her on the cot.

"It was one of those two guys who we took out, wasn't it?" she asked. "I mean, that's my best guess, although I thought they were unconscious. I know at least your guy was. Not sure about mine anymore."

He shook his head solemnly and gave her hand a small squeeze of comfort. "You have no idea how much I wish it was one of them, but it wasn't."

"Leo, who did it? Was there another one?"

Saying the next three words was an incredible effort. "It was Simmons."

Skye stared at him, rigid in disbelief. She looked like she was about to cry. "What?" she whispered hoarsely.

"When I was looking at the wall, because of…the blood," Leo explained as a strong wave of guilt crashed over him. He hadn't been looking, and only made it easier for Simmons to carry out her plan. It was his fault they were here. He continued with a heavy heart. "I thought about something. I realized that we should have heard a gunshot, but we didn't, Skye. We just heard scream, and those guns, they didn't have silencers. I noticed this and when I turned around, you were in the ground. Simmons was standing over you, holding a baton."

"She knocked me out?" murmured Skye. Tears were beginning to appear in her eyes. "But she got shot!"

Leo shook his head. "I saw her side. There was no wound, it was just fake blood. I asked what was going on when she started to come closer to me. She wasn't the Simmons I know, the one we know. She was dark, and sinister and creepy and it scared me. Not even Ward scared me as much as she did. She told me that I would understand one day just before she took me out. But the way she said it…., Skye I don't think I want to know what it is."

"No," Skye cried, wiping her eyes angrily. "No no no, stop it! Leo, it can't be true!"

All Leo wanted to do was turn away in shame. He had seen the darkness Simmons harbored himself, but Skye hadn't. No matter how much he wanted things to not be this way, this was what they were, and there was nothing that could be done besides accepting them.

"I'm sorry. I'm so sorry, Skye," he told her. "But it is. Simmons is-"

"DON' SAY IT!" Skye screamed, jumping up from the cot, fist balled in anger. "SHE CAN'T BE, LEO. SHE JUST CAN'T!"

"Why not!" Leo shot back, standing up to face her eye to eye. "Why not, Skye? Give me a reason for it, any reason, but just tell me. Why. Not."

"Because," Skye faltered. "Because…."

She stopped and broke down in sobs. Leo wrapped his arms around her, feeling every wracking sob shake him. He lowered the two of them down together onto the floor, and permitted a few of his own tears to fall. He and Simmons had been through so much together, both good and bad, and he had trusted her with his life so many times. But right now, his faith in her was gone like breathe on a mirror. She was only a traitor in his eyes now.

"I didn't mean to yell," Leo apologized after Skye had quieted down. His shoulder felt damp, but that was the least of his concerns.

"S'okay," Skye's voice was a little muffled in his shirt. "But Simmons, she can't be-"

The heavy steel door clanged open and cut her off. The pair looked up and watched as two people entered in their cell. The first one, a man, was tall and muscular. His arms were peppered with thin little scars, but his right one was peculiar and caught Leo's attention. The lower arm (and, Leo assumed, the gloved hand) was an unnatural shade of dark purple, and parts of the purple looked to be slowly snaking up his veins. The woman with him had dark skin that made her acidic green eyes stand out even more than they already did. Beside him, Skye gulped nervously.

Then a third person entered the room, and Leo's world stilled.

Jemma Simmons strode in confidently as he ogled her, paralyzed in shock. She was dressed differently than usual, wearing a black sweater, a short red skirt, and high heels. The Simmons he knew never ever wore high heels, but she moved about in them with ease. She wore a white lab coat over the sweater, and it reassured Leo a tiny bit to see that there was no symbol for Hydra on it. Of all the things she'd ever told him, at least the one about her not being Hydra was true, or at least he hoped it was.

"Well," Simmons said breezily, giving the two of them a small, dark smile. "It's nice to see you up, Fitz. You too, Skye."

"Simmons?" Skye's voice was barely audible. "No, you can't be. You're an agent of SHIELD, not…not this."

The biochemist chuckled. "Oh, Skye. Didn't Fitz tell you? I know he saw me. I'm not loyal to SHIELD, never was. But I am loyal to the Doctor, and he wants to see you."

"The Doctor?" Skye frowned, shifting forward. "Doctor Who?"

"Just the Doctor, dear," Simmons replied. "He has a few other names, but that's one of his more professional titles."

Leo wisely resisted the urge to snicker, and found it squashed completely when the man stepped forward and pulled Skye away from him. "Hey," he shouted as the party began to exit. "Let her go!"

"Leo!" cried Skye as Jemma stepped between them and pulled out a gun. Leo stared at it in shock. It was like the early Night-Night Guns, except the frame was black and green glowed on the sides. Still, he climbed to his feet.

"You always have to be so aggravatingly stubborn, don't you," Simmons hissed. "I really thought you'd understand by now that I mean business."

She pulled the trigger, and Skye screamed. Something struck him in the forehead, and Leo felt himself fall to the ground as the world once again went black.

* * *

**Ha ha, Cliffhanger! I'm sorry, but not sorry. I am scared of my own creation of Dark Jemma though.**

**Good news is that I've already made good progress on the next chapter, so you'll find out what happens when Skye meets her father.**

**Thoughts?**


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